Publications
| Title | Abstract | Year(sorted descending) Filter | PMID Filter |
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| functional relevance of j-protein family of rice (oryza sativa). | protein folding and disaggregation are crucial processes for survival of cells under unfavorable conditions. a network of molecular chaperones supports these processes. collaborative action of hsp70 and hsp100 proteins is an important component of this network. j-proteins/dnaj members as co-chaperones assist hsp70. as against 22 dnaj sequences noted in yeast, rice genome contains 104 j-genes. rice j-genes were systematically classified into type a (12 sequences), type b (9 sequences), and type c ... | 2013 | 23160806 |
| thai herbal formulas used for wound treatment: a study of their antibacterial potency, anti-inflammatory, antioxidant, and cytotoxicity effects. | this present work was aimed to investigate wound healing-related biologic activities of traditional herbal formulas used for wound treatment in southern thailand. | 2013 | 23363309 |
| sui-family genes encode phosphatidylserine synthases and regulate stem development in rice. | in vascular plants, the regulation of stem cell niche determines development of aerial shoot which consists of stems and lateral organs. intercalary meristem (im) controls internode elongation in rice and other grasses, however little attention has been paid to the underlying mechanism of stem cell maintenance. here, we investigated the stem development in rice and showed that the shortened uppermost internode 1 (sui1) family of genes are pivotal for development of rice stems. we demonstrated th ... | 2013 | 22956125 |
| expression analysis of rice vq genes in response to biotic and abiotic stresses. | wrky transcription factors are encoded by a large gene superfamily with a broad range of roles in plants. proteins containing a short vq (fxxxvqxltg) motif have been recently shown to interact with wrky transcription factors, implying that atvq proteins are important in the plant defense responses in arabidopsis, either as positive or negative cofactors of wrky transcription factors. thirty-nine oryza sativa genes containing the vq motif (osvqs) were identified and the genome structures of osvq ... | 2013 | 23958655 |
| down-regulation of ossag12-1 results in enhanced senescence and pathogen-induced cell death in transgenic rice plants. | senescence is a highly regulated process accompanied by changes in gene expression. while the mrna levels of most genes decline, the mrna levels of specific genes (senescence associated genes, sags) increase during senescence. arabidopsis sag12 (atsag12) gene codes for papain-like cysteine protease. the promoter of atsag12 is sa-responsive and reported to be useful to delay senescence by expressing cytokinin biosynthesis gene isopentenyltransferase specifically during senescence in several plant ... | 2013 | 23938390 |
| a mutation in the xanthomonas oryzae pv. oryzae wxod gene affects xanthan production and chemotaxis. | xanthomonas oryzae pv. oryzae causes bacterial blight in rice (oryza sativa l.). the effect of a mutation in the wxod gene, that encodes a putative o-antigen acetylase, on xanthan production as well as bacterial chemotaxis was investigated. the mutation increased xanthan production by 52 %. the mutant strain was non-motile on semi-solid agar swarm plates. in addition, several genes involved in chemotaxis, including the chew, chev, cher, and ched genes, were down-regulated by a mutation in the wx ... | 2013 | 23881323 |
| analysis of transcript and metabolite levels in italian rice (oryza sativa l.) cultivars subjected to osmotic stress or benzothiadiazole treatment. | one of the major objectives of rice (oryza sativa l.) breeding programs is the development of new varieties with higher tolerance/resistance to both abiotic and biotic stresses. in this study, italian rice cultivars were subjected to osmotic stress or benzothiadiazole (bth) treatments. an analysis of the expression of selected genes known to be involved in the stress response and (1)h nuclear magnetic resonance ((1)h nmr) metabolic profiling were combined with multivariate statistical analyses t ... | 2013 | 23860229 |
| analysis of nucleotide diversity among alleles of the major bacterial blight resistance gene xa27 in cultivars of rice (oryza sativa) and its wild relatives. | xa27 is one of the important r-genes, effective against bacterial blight disease of rice caused by xanthomonas oryzae pv. oryzae (xoo). using natural population of oryza, we analyzed the sequence variation in the functionally important domains of xa27 across the oryza species. dna sequences of xa27 alleles from 27 rice accessions revealed higher nucleotide diversity among the reported r-genes of rice. sequence polymorphism analysis revealed synonymous and non-synonymous mutations in addition to ... | 2013 | 23652799 |
| the xa21 binding protein xb25 is required for maintaining xa21-mediated disease resistance. | plant genomes encode a large number of proteins that potentially function as immune receptors in the defense against pathogen invasion. as a well-characterized receptor kinase consisting of 23 tandem leucine-rich repeats, a transmembrane domain and a serine/threonine kinase, the rice (oryza sativa) protein xa21 confers resistance to a broad spectrum of xanthomonas oryzae pv. oryzae (xoo) races that cause bacterial blight disease. we report here that xa21 binding protein 25 (xb25) belongs to the ... | 2013 | 23206229 |
| involvement of mitogen activated protein kinase kinase 6 in uv induced transcripts accumulation of genes in phytoalexin biosynthesis in rice. | ultra violet radiation leads to accumulation of phytoalexins (pa) in rice (oryza sativa) which are typically accumulated when the plants are infected with rice blast pathogen magnaporthe oryzae. although extensive works have been done in elucidating phytoalexin biosynthesis, uv stress signal transduction leading to accumulations of rice phytoalexin is largely unknown. | 2013 | 24295067 |
| identification of a novel microrna (mirna) from rice that targets an alternatively spliced transcript of the nramp6 (natural resistance-associated macrophage protein 6) gene involved in pathogen resistance. | plants have evolved efficient defence mechanisms to defend themselves from pathogen attack. although many studies have focused on the transcriptional regulation of defence responses, less is known about the involvement of micrornas (mirnas) as post-transcriptional regulators of gene expression in plant immunity. this work investigates mirnas that are regulated by elicitors from the blast fungus magnaporthe oryzae in rice (oryza sativa). small rna libraries were constructed from rice tissues and ... | 2013 | 23627500 |
| structural and functional study in the rhizosphere of oryza sativa l. plants growing under biotic and abiotic stress. | a structural and functional study has been carried out in the rice production area of the guadalquivir marshes in southern spain aiming to increase knowledge of rice rhizosphere structure and function for further application on integrated management practices. | 2013 | 23594253 |
| constitutive expression of a mir319 gene alters plant development and enhances salt and drought tolerance in transgenic creeping bentgrass. | microrna319 (mir319) is one of the first characterized and conserved microrna families in plants and has been demonstrated to target tcp (for teosinte branched/cycloidea/proliferating cell factors [pcf]) genes encoding plant-specific transcription factors. mir319 expression is regulated by environmental stimuli, suggesting its involvement in plant stress response, although experimental evidence is lacking and the underlying mechanism remains elusive. this study investigates the role that mir319 ... | 2013 | 23292790 |
| proteomic insights into seed germination in response to environmental factors. | seed germination is a critical process in the life cycle of higher plants. during germination, the imbibed mature seed is highly sensitive to different environmental factors.however, knowledge about the molecular and physiological mechanisms underlying the environmental effects on germination has been lacking. recent proteomic work has provided invaluable insight into the molecular processes in germinating seeds of arabidopsis, rice (oryza sativa), soybean (glycine max), barley (hordeum vulgare) ... | 2013 | 23986916 |
| transgenic rice with inducible ethylene production exhibits broad-spectrum disease resistance to the fungal pathogens magnaporthe oryzae and rhizoctonia solani. | rice blast (magnaporthe oryzae) and sheath blight (rhizoctonia solani) are the two most devastating diseases of rice (oryza sativa), and have severe impacts on crop yield and grain quality. recent evidence suggests that ethylene (et) may play a more prominent role than salicylic acid and jasmonic acid in mediating rice disease resistance. in this study, we attempt to genetically manipulate endogenous et levels in rice for enhancing resistance to rice blast and sheath blight diseases. transgenic ... | 2013 | 23031077 |
| cross-species analysis of genic gc3 content and dna methylation patterns. | the gc content in the third codon position (gc(3)) exhibits a unimodal distribution in many plant and animal genomes. interestingly, grasses and homeotherm vertebrates exhibit a unique bimodal distribution. high gc(3) was previously found to be associated with variable expression, higher frequency of upstream tata boxes, and an increase of gc(3) from 5' to 3'. moreover, gc(3)-rich genes are predominant in certain gene classes and are enriched in cpg dinucleotides that are potential targets for m ... | 2013 | 23833164 |
| dissection of two major components of the post-zygotic hybridization barrier in rice endosperm. | a post-zygotic hybridization barrier is often observed in the endosperm of seeds produced by interspecific or interploidy crosses. in arabidopsis thaliana, for example, hybrid endosperm from both types of cross shows altered timing of cellularization and an altered rate of nuclear divisions. therefore, it has been proposed that interspecific and interploidy crosses share common molecular mechanisms for establishment of an effective species barrier. however, these two types of hybridization barri ... | 2013 | 24286595 |
| introns targeted by plant micrornas: a possible novel mechanism of gene regulation. | in plant cells, most micrornas (mirnas) perform cleavages of target mature mrnas in the cytoplasm. a recent report of a mirna pathway involved in dna methylation in the rice nucleus raises the possibility that plant mirnas could cleave intron-containing pre-mrnas (the precursor of messenger rnas) located in the nucleus. | 2013 | 24280590 |
| wikipathways for plants: a community pathway curation portal and a case study in rice and arabidopsis seed development networks. | next-generation sequencing and 'omics' platforms are used extensively in plant biology research to unravel new genomes and study their interactions with abiotic and biotic agents in the growth environment. despite the availability of a large and growing number of genomic data sets, there are only limited resources providing highly-curated and up-to-date metabolic and regulatory networks for plant pathways. | 2013 | 24280312 |
| development of a novel prediction method of cis-elements to hypothesize collaborative functions of cis-element pairs in iron-deficient rice. | cis-acting elements are essential genomic sequences that control gene expression. in higher eukaryotes, a series of cis-elements function cooperatively. however, further studies are required to examine the co-regulation of multiple cis-elements on a promoter. the aim of this study was to propose a model of cis-element networks that cooperatively regulate gene expression in rice under iron (fe) deficiency. | 2013 | 24279975 |
| the distribution of different classes of nuclear localization signals (nlss) in diverse organisms and the utilization of the minor nls-binding site inplantnuclear import factor importin-α. | the specific recognition between the import receptor importin-α and the nuclear localization signals (nlss) is crucial to ensure the selective transport of cargoes into the nucleus. nlss contain 1 or 2 clusters of positively charged amino acids, which usually bind to the major (monopartite nlss) or both minor and major nls-binding sites (bipartite nlss). in our recent study, we determined the structure of importin-α1a from rice (oryza sativa), and made 2 observations that suggest an increased ut ... | 2013 | 24270630 |
| maize lazy1 mediates shoot gravitropism and inflorescence development through regulating auxin transport, auxin signaling, and light response. | auxin is a plant hormone that plays key roles in both shoot gravitropism and inflorescence development. however, these two processes appear to be parallel and to be regulated by distinct players. here, we report that the maize (zea mays) prostrate stem1 mutant, which is allelic to the classic mutant lazy plant1 (la1), displays prostrate growth with reduced shoot gravitropism and defective inflorescence development. map-based cloning identified maize zmla1 as the functional ortholog of lazy1 in r ... | 2013 | 24089437 |
| survey of genes involved in rice secondary cell wall formation through a co-expression network. | the plant secondary cell wall is the major source of lignocellulosic biomass, a renewable energy resource that can be used for bioethanol production. to comprehensively identify transcription factors (tfs), glycosyltransferase (gt) and glycosyl hydrolase (gh) involved in secondary cell wall formation in rice (oryza sativa), co-expression network analysis was performed using 68 microarray data points for different rice tissues and stages. in addition to rice genes encoding orthologs of arabidopsi ... | 2013 | 24089433 |
| root transcript profiling of two rorippa species reveals gene clusters associated with extreme submergence tolerance. | complete submergence represses photosynthesis and aerobic respiration, causing rapid mortality in most terrestrial plants. however, some plants have evolved traits allowing them to survive prolonged flooding, such as species of the genus rorippa, close relatives of arabidopsis (arabidopsis thaliana). we studied plant survival, changes in carbohydrate and metabolite concentrations, and transcriptome responses to submergence of two species, rorippa sylvestris and rorippa amphibia. we exploited the ... | 2013 | 24077074 |
| roles of pollen-specific boron efflux transporter, osbor4, in the rice fertilization process. | arabidopsis thaliana bor1 was the first boron (b) transporter identified in living systems. there are four atbor1-like genes, osbor1, 2, 3 and 4, present in the rice genome. we characterized the activity, expression and physiological function of osbor4. osbor4 is an active efflux transporter of b. quantitative pcr analysis and osbor4 promoter-green fluorescent protein (gfp) fusion revealed that osbor4 was both highly and specifically expressed in pollen. we obtained five tos17 insertion mutants ... | 2013 | 24068795 |
| nitrogen-dependent regulation of de novo cytokinin biosynthesis in rice: the role of glutamine metabolism as an additional signal. | cytokinin activity in plants is closely related to nitrogen availability, and an arabidopsis gene for adenosine phosphate-isopentenyltransferase (ipt), ipt3, is regulated by inorganic nitrogen sources in a nitrate-specific manner. in this study, we have identified another regulatory system of cytokinin de novo biosynthesis in response to nitrogen status. in rice, osipt4, osipt5, osipt7 and osipt8 were up-regulated in response to exogenously applied nitrate and ammonium, with accompanying accumul ... | 2013 | 24058148 |
| the ubiquitin receptor da1 interacts with the e3 ubiquitin ligase da2 to regulate seed and organ size in arabidopsis. | seed size in higher plants is determined by the coordinated growth of the embryo, endosperm, and maternal tissue. several factors that act maternally to regulate seed size have been identified, such as auxin response factor2, apetala2, kluh, and da1, but the genetic and molecular mechanisms of these factors in seed size control are almost totally unknown. we previously demonstrated that the ubiquitin receptor da1 acts synergistically with the e3 ubiquitin ligase enhancer1 of da1 (eod1)/big broth ... | 2013 | 24045020 |
| selective acquisition and retention of genomic sequences by pack-mutator-like elements based on guanine-cytosine content and the breadth of expression. | the process of gene duplication followed by sequence and functional divergence is important for the generation of new genes. pack-mules, nonautonomous mutator-like elements (mules) that carry genic sequence(s), are potentially involved in generating new open reading frames and regulating parental gene expression. these elements are identified in many plant genomes and are most abundant in rice (oryza sativa). despite the abundance of pack-mules, the mechanism by which parental genes are captured ... | 2013 | 24028844 |
| subfunctionalization of sigma factors during the evolution of land plants based on mutant analysis of liverwort (marchantia polymorpha l.) mpsig1. | sigma factor is a subunit of plastid-encoded rna polymerase that regulates the transcription of plastid-encoded genes by recognizing a set of promoters. sigma factors have increased in copy number and have diversified during the evolution of land plants, but details of this process remain unknown. liverworts represent the basal group of embryophytes and are expected to retain the ancestral features of land plants. in liverwort (marchantia polymorpha l.), we isolated and characterized a t-dna-tag ... | 2013 | 24025801 |
| perturbation of brachypodium distachyon cellulose synthase a4 or 7 results in abnormal cell walls. | cellulose is an integral component of the plant cell wall and accounts for approximately forty percent of total plant biomass but understanding its mechanism of synthesis remains elusive. cellulose synthase a (cesa) proteins function as catalytic subunits of a rosette-shaped complex that synthesizes cellulose at the plasma membrane. arabidopsis thaliana and rice (oryza sativa) secondary wall cesa loss-of-function mutants have weak stems and irregular or thin cell walls. | 2013 | 24024469 |
| genome-wide prediction of traits with different genetic architecture through efficient variable selection. | in genome-based prediction there is considerable uncertainty about the statistical model and method required to maximize prediction accuracy. for traits influenced by a small number of quantitative trait loci (qtl), predictions are expected to benefit from methods performing variable selection [e.g., bayesb or the least absolute shrinkage and selection operator (lasso)] compared to methods distributing effects across the genome [ridge regression best linear unbiased prediction (rr-blup)]. we inv ... | 2013 | 23934883 |
| identification and characterization of osebs, a gene involved in enhanced plant biomass and spikelet number in rice. | common wild rice (oryza rufipogon griff.) is an important genetic reservoir for rice improvement. we investigated a quantitative trait locus (qtl), qgp5-1, which is related to plant height, leaf size and panicle architecture, using a set of introgression lines of o. rufipogon in the background of the indica cultivar guichao2 (oryza sativa l.). we cloned and characterized qgp5-1 and confirmed that the newly identified gene osebs (enhancing biomass and spikelet number) increased plant height, leaf ... | 2013 | 23924074 |
| evaluation of genome sequencing quality in selected plant species using expressed sequence tags. | with the completion of genome sequencing projects for more than 30 plant species, large volumes of genome sequences have been produced and stored in online databases. advancements in sequencing technologies have reduced the cost and time of whole genome sequencing enabling more and more plants to be subjected to genome sequencing. despite this, genome sequence qualities of multiple plants have not been evaluated. | 2013 | 23922843 |
| hormone defense networking in rice: tales from a different world. | recent advances in plant immunity research underpin the pivotal role of small-molecule hormones in regulating the plant defense signaling network. although most of our understanding comes from studies of dicot plants such as arabidopsis thaliana, new studies in monocots are providing additional insights into the defense-regulatory role of phytohormones. here, we review the roles of both classical and more recently identified stress hormones in regulating immunity in the model monocot rice (oryza ... | 2013 | 23910453 |
| how protein targeting to primary plastids via the endomembrane system could have evolved? a new hypothesis based on phylogenetic studies. | it is commonly assumed that a heterotrophic ancestor of the supergroup archaeplastida/plantae engulfed a cyanobacterium that was transformed into a primary plastid; however, it is still unclear how nuclear-encoded proteins initially were imported into the new organelle. most proteins targeted to primary plastids carry a transit peptide and are transported post-translationally using toc and tic translocons. there are, however, several proteins with n-terminal signal peptides that are directed to ... | 2013 | 23845039 |
| on the cellular site of two-pore channel tpc1 action in the poaceae. | the slow vacuolar (sv) channel has been characterized in different dicots by patch-clamp recordings. this channel represents the major cation conductance of the largest organelle in most plant cells. studies with the tpc1-2 mutant of the model dicot plant arabidopsis thaliana identified the sv channel as the product of the tpc1 gene. by contrast, research on rice and wheat tpc1 suggested that the monocot gene encodes a plasma membrane calcium-permeable channel. to explore the site of action of g ... | 2013 | 23845012 |
| flooding tolerance: o2 sensing and survival strategies. | the investigation of flooding survival strategies in model, crop and wild plant species has yielded insights into molecular, physiological and developmental mechanisms of soil flooding (waterlogging) and submergence survival. the antithetical flooding escape and quiescence strategies of deepwater and submergence tolerant rice (oryza sativa), respectively, are regulated by members of a clade of ethylene responsive factor transcriptional activators. this knowledge paved the way for the discovery t ... | 2013 | 23830867 |
| the arabidopsis thaliana myb60 promoter provides a tool for the spatio-temporal control of gene expression in stomatal guard cells. | plants have evolved different strategies to resist drought, of which the best understood is the abscisic acid (aba)-induced closure of stomatal pores to reduce water loss by transpiration. the availability of useful promoters that allow for precise spatial and temporal control of gene expression in stomata is essential both for investigating stomatal regulation in model systems and for biotechnological applications in field crops. previous work indicated that the regulatory region of the transcr ... | 2013 | 23828545 |
| an improved simplified high-sensitivity quantification method for determining brassinosteroids in different tissues of rice and arabidopsis. | quantification of brassinosteroids is essential and extremely important to study the molecular mechanisms of their physiological roles in plant growth and development. herein, we present a simple, material and cost-saving high-performance method for determining endogenous brassinosteroids (brs) in model plants. this new method enables simultaneous enrichment of a wide range of bioactive brs such as brassinolide, castasterone, teasterone, and typhasterol with ion exchange solid-phase extraction a ... | 2013 | 23800992 |
| brachypodium distachyon as a model plant toward improved biofuel crops: search for secreted proteins involved in biogenesis and disassembly of cell wall polymers. | polysaccharides make up about 75% of plant cell walls and can be broken down to produce sugar substrates (saccharification) from which a whole range of products can be obtained, including bioethanol. cell walls also contain 5-10% of proteins, which could be used to tailor them for agroindustrial uses. here we present cell wall proteomics data of brachypodium distachyon, a model plant for temperate grasses. leaves and culms were analyzed during active growth and at mature stage. altogether, 559 p ... | 2013 | 23784962 |
| analysis of rice snf2 family proteins and their potential roles in epigenetic regulation. | snf2 family proteins are atp-dependent chromatin remodeling factors that control many aspects of dna events such as transcription, replication, homologous recombination and dna repair. in animals several members in this family have been revealed to control gene expression in concert with other epigenetic mechanisms including histone modification, histone variants and dna methylation. their function in regulating genome expression in plant has hardly been disclosed before except in arabidopsis. h ... | 2013 | 23770592 |
| rootnav: navigating images of complex root architectures. | we present a novel image analysis tool that allows the semiautomated quantification of complex root system architectures in a range of plant species grown and imaged in a variety of ways. the automatic component of rootnav takes a top-down approach, utilizing the powerful expectation maximization classification algorithm to examine regions of the input image, calculating the likelihood that given pixels correspond to roots. this information is used as the basis for an optimization approach to ro ... | 2013 | 23766367 |
| arabidopsis enhanced drought tolerance1/homeodomain glabrous11 confers drought tolerance in transgenic rice without yield penalty. | enhancing drought tolerance without yield decrease has been a great challenge in crop improvement. here, we report the arabidopsis (arabidopsis thaliana) homodomain-leucine zipper transcription factor enhanced drought tolerance/homeodomain glabrous11 (edt1/hdg11) was able to confer drought tolerance and increase grain yield in transgenic rice (oryza sativa) plants. the improved drought tolerance was associated with a more extensive root system, reduced stomatal density, and higher water use effi ... | 2013 | 23735506 |
| planex: the plant co-expression database. | the plant co-expression database (planex) is a new internet-based database for plant gene analysis. planex (http://planex.plantbioinformatics.org) contains publicly available genechip data obtained from the gene expression omnibus (geo) of the national center for biotechnology information (ncbi). planex is a genome-wide co-expression database, which allows for the functional identification of genes from a wide variety of experimental designs. it can be used for the characterization of genes for ... | 2013 | 23688397 |
| conservation, divergence, and genome-wide distribution of pal and pox a gene families in plants. | genome-wide identification and phylogenetic and syntenic comparison were performed for the genes responsible for phenylalanine ammonia lyase (pal) and peroxidase a (pox a) enzymes in nine plant species representing very diverse groups like legumes (glycine max and medicago truncatula), fruits (vitis vinifera), cereals (sorghum bicolor, zea mays, and oryza sativa), trees (populus trichocarpa), and model dicot (arabidopsis thaliana) and monocot (brachypodium distachyon) species. a total of 87 and ... | 2013 | 23671845 |
| ppetac1 promotes the horizontal growth of branches in peach trees and is a member of a functionally conserved gene family found in diverse plants species. | trees are capable of tremendous architectural plasticity, allowing them to maximize their light exposure under highly competitive environments. one key component of tree architecture is the branch angle, yet little is known about the molecular basis for the spatial patterning of branches in trees. here, we report the identification of a candidate gene for the br mutation in prunus persica (peach) associated with vertically oriented growth of branches, referred to as 'pillar' or 'broomy'. ppa0100 ... | 2013 | 23663106 |
| dbwfa: a web-based database for functional annotation of triticum aestivum transcripts. | the functional annotation of genes based on sequence homology with genes from model species genomes is time-consuming because it is necessary to mine several unrelated databases. the aim of the present work was to develop a functional annotation database for common wheat triticum aestivum (l.). the database, named dbwfa, is based on the reference ncbi unigene set, an expressed gene catalogue built by expressed sequence tag clustering, and on full-length coding sequences retrieved from the trifld ... | 2013 | 23660284 |
| kinetics and functional diversity among the five members of the nadp-malic enzyme family from zea mays, a c4 species. | nadp-malic enzyme (nadp-me) is involved in different metabolic pathways in several organisms due to the relevant physiological functions of the substrates and products of its reaction. in plants, it is one of the most important proteins that were recruited to fulfil key roles in c4 photosynthesis. recent advances in genomics allowed the characterization of the complete set of nadp-me genes from some c3 species, as arabidopsis thaliana and oryza sativa; however, the characterization of the comple ... | 2013 | 23649167 |
| comprehensive protein-based artificial microrna screens for effective gene silencing in plants. | artificial microrna (amirna) approaches offer a powerful strategy for targeted gene manipulation in any plant species. however, the current unpredictability of amirna efficacy has limited broad application of this promising technology. to address this, we developed epitope-tagged protein-based amirna (etpamir) screens, in which target mrnas encoding epitope-tagged proteins were constitutively or inducibly coexpressed in protoplasts with amirna candidates targeting single or multiple genes. this ... | 2013 | 23645631 |
| phylogeny and a structural model of plant mhx transporters. | the arabidopsis thaliana mhx gene (atmhx) encodes a mg²⁺/h⁺ exchanger. among non-plant proteins, atmhx showed the highest similarity to mammalian na⁺/ca²⁺ exchanger (ncx) transporters, which are part of the ca²⁺/cation (caca) exchanger superfamily. | 2013 | 23634958 |
| plantgsea: a gene set enrichment analysis toolkit for plant community. | gene set enrichment analysis (gsea) is a powerful method for interpreting biological meaning of a list of genes by computing the overlaps with various previously defined gene sets. as one of the most widely used annotations for defining gene sets, gene ontology (go) system has been used in many enrichment analysis tools. easygo and agrigo, two go enrichment analysis toolkits developed by our laboratory, have gained extensive usage and citations since their releases because of their effective per ... | 2013 | 23632162 |
| collapsed abnormal pollen1 gene encoding the arabinokinase-like protein is involved in pollen development in rice. | we isolated a pollen-defective mutant, collapsed abnormal pollen1 (cap1), from tos17 insertional mutant lines of rice (oryza sativa). the cap1 heterozygous plant produced equal numbers of normal and collapsed abnormal grains. the abnormal pollen grains lacked almost all cytoplasmic materials, nuclei, and intine cell walls and did not germinate. genetic analysis of crosses revealed that the cap1 mutation did not affect female reproduction or vegetative growth. cap1 encodes a protein consisting of ... | 2013 | 23629836 |
| α-tubulin is rapidly phosphorylated in response to hyperosmotic stress in rice and arabidopsis. | by using high-resolution two-dimensional page followed by phosphoprotein-specific staining and peptide mass fingerprint analysis along with other assays, we found that α-tubulin is phosphorylated in response to hyperosmotic stress in rice and arabidopsis. the onset of the phosphorylation response was as early as 2 min after hyperosmotic stress treatment, and a major proportion of α-tubulin was phosphorylated after 60 min in root tissues. however, the phosphorylated form of α-tubulin was readily ... | 2013 | 23628996 |
| genome-wide analysis of the expansin gene superfamily reveals grapevine-specific structural and functional characteristics. | expansins are proteins that loosen plant cell walls in a ph-dependent manner, probably by increasing the relative movement among polymers thus causing irreversible expansion. the expansin superfamily (exp) comprises four distinct families: expansin a (expa), expansin b (expb), expansin-like a (exla) and expansin-like b (exlb). there is experimental evidence that expa and expb proteins are required for cell expansion and developmental processes involving cell wall modification, whereas the exact ... | 2013 | 23614035 |
| functional conservation of mikc*-type mads box genes in arabidopsis and rice pollen maturation. | there are two groups of mads intervening keratin-like and c-terminal (mikc)-type mads box genes, mikc(c) type and mikc* type. in seed plants, the mikc(c) type shows considerable diversity, but the mikc* type has only two subgroups, p- and s-clade, which show conserved expression in the gametophyte. to examine the functional conservation of mikc*-type genes, we characterized all three rice (oryza sativa) mikc*-type genes. all three genes are specifically expressed late in pollen development. the ... | 2013 | 23613199 |
| roles of plant hormones and their interplay in rice immunity. | plant hormones have been extensively studied for their importance in innate immunity particularly in the dicotyledonous model plant arabidopsis thaliana. however, only in the last decade, plant hormones were demonstrated to play conserved and divergent roles in fine-tuning immune in rice (oryza sativa l.), a monocotyledonous model crop plant. emerging evidence showed that salicylic acid (sa) plays a role in rice basal defense but is differentially required by rice pattern recognition receptor (p ... | 2013 | 23589608 |
| a guanine nucleotide exchange factor for rab5 proteins is essential for intracellular transport of the proglutelin from the golgi apparatus to the protein storage vacuole in rice endosperm. | rice (oryza sativa) glutelins are synthesized on the endoplasmic reticulum as a precursor, which are then transported via the golgi to protein storage vacuoles (psvs), where they are proteolytically processed into acidic and basic subunits. the glutelin precursor mutant6 (glup6) accumulates abnormally large amounts of proglutelin. map-base cloning studies showed that glup6 was a loss-of-function mutant of guanine nucleotide exchange factor (gef), which activates rab gtpase, a key regulator of me ... | 2013 | 23580596 |
| a significant fraction of 21-nucleotide small rna originates from phased degradation of resistance genes in several perennial species. | small rnas (srnas), including microrna (mirna) and short-interfering rna (sirna), are important in the regulation of diverse biological processes. comparative studies of srnas from plants have mainly focused on mirna, even though they constitute a mere fraction of the total srna diversity. in this study, we report results from an in-depth analysis of the srna population from the conifer spruce (picea abies) and compared the results with those of a range of plant species. the vast majority of srn ... | 2013 | 23580593 |
| clock-controlled and flowering locus t (ft)-dependent photoperiodic pathway in lotus japonicus i: verification of the flowering-associated function of an ft homolog. | during the last decade, significant research progress in the study of arabidopsis thaliana has been made in defining the molecular mechanism by which the plant circadian clock regulates flowering time in response to changes in photoperiod. it is generally accepted that the clock-controlled constans (co)-flowering locus t (ft)-mediated external coincidence mechanism underlying the photoperiodic control of flowering time is conserved in higher plants, including a. thaliana and oryza sativa. howeve ... | 2013 | 23563564 |
| the evolution and diversification of plant microtubule-associated proteins. | plant evolution is marked by major advances in structural characteristics that facilitated the highly successful colonization of dry land. underlying these advances is the evolution of genes encoding specialized proteins that form novel microtubular arrays of the cytoskeleton. this review investigates the evolution of plant families of microtubule-associated proteins (maps) through the recently sequenced genomes of arabidopsis thaliana, oryza sativa, selaginella moellendorffii, physcomitrella pa ... | 2013 | 23551562 |
| a conserved genetic pathway determines inflorescence architecture in arabidopsis and rice. | the spatiotemporal architecture of inflorescences that bear flowers determines plant reproductive success by affecting fruit set and plant interaction with pollinators. the inflorescence architecture that displays great diversity across flowering plants depends on developmental decisions at inflorescence meristems. here we report a key conserved genetic pathway determining inflorescence architecture in arabidopsis thaliana and oryza sativa (rice). in arabidopsis, four mads-box genes, suppressor ... | 2013 | 23537632 |
| methionine salvage and s-adenosylmethionine: essential links between sulfur, ethylene and polyamine biosynthesis. | both met (methionine) and sam (s-adenosylmethionine), the activated form of met, participate in a number of essential metabolic pathways in plants. the subcellular compartmentalization of met fluxes will be discussed in the present review with respect to regulation and communication with the sulfur assimilation pathway, the network of the aspartate-derived amino acids and the demand for production of sam. sam enters the ethylene, nicotianamine and polyamine biosynthetic pathways and provides the ... | 2013 | 23535167 |
| patterns and evolution of acgt repeat cis-element landscape across four plant genomes. | transcription factor binding is regulated by several interactions, primarily involving cis-element binding. these binding sites maintain specificity by means of their sequence, and other additional factors such as inter-motif distance and spacer specificity. the acgt core sequence has been established as a functionally important cis-element which frequently regulates gene expression in synergy with other cis-elements. in this study, we used two monocotyledonous - oryza sativa and sorghum bicolor ... | 2013 | 23530833 |
| in silico comparative analysis and expression profile of antioxidant proteins in plants. | the antioxidant system in plants is a very important defensive mechanism to overcome stress conditions. we examined the expression profile of antioxidant enzymes superoxide dismutase (sod), catalase (cat) and ascorbate peroxidase (apx) using a bioinformatics approach. we explored secondary structure prediction and made detailed studies of signature pattern of antioxidant proteins in four plant species (triticum aestivum, arabidopsis thaliana, oryza sativa, and brassica juncea). fingerprinting an ... | 2013 | 23512671 |
| paraquat resistant1, a golgi-localized putative transporter protein, is involved in intracellular transport of paraquat. | paraquat is one of the most widely used herbicides worldwide. in green plants, paraquat targets the chloroplast by transferring electrons from photosystem i to molecular oxygen to generate toxic reactive oxygen species, which efficiently induce membrane damage and cell death. a number of paraquat-resistant biotypes of weeds and arabidopsis (arabidopsis thaliana) mutants have been identified. the herbicide resistance in arabidopsis is partly attributed to a reduced uptake of paraquat through plas ... | 2013 | 23471133 |
| genome-wide computational prediction and analysis of core promoter elements across plant monocots and dicots. | transcription initiation, essential to gene expression regulation, involves recruitment of basal transcription factors to the core promoter elements (cpes). the distribution of currently known cpes across plant genomes is largely unknown. this is the first large scale genome-wide report on the computational prediction of cpes across eight plant genomes to help better understand the transcription initiation complex assembly. the distribution of thirteen known cpes across four monocots (brachypodi ... | 2013 | 24205361 |
| high-throughput analysis of rice genes by means of the heterologous full-length cdna overexpressor (fox)-hunting system. | mutant populations are indispensable tools for investigating plant gene functions. gain-of-function technology is one of the approaches used for the systematic production of mutant resources and activation tagging is a well-established method to generate gain-of-function mutants in plants. as an alternative approach for the systematic generation of a gain-of-function mutant population, we developed the full-length cdna overexpressor (fox)-hunting system in which full-length cdnas (fl-cdnas) are ... | 2013 | 24166434 |
| overexpression of a partial fragment of the salt-responsive gene osnuc1 enhances salt adaptation in transgenic arabidopsis thaliana and rice (oryza sativa l.) during salt stress. | the rice (oryza sativa l.) nucleolin gene, osnuc1, transcripts were expressed in rice leaves, flowers, seeds and roots but differentially expressed within and between two pairs of salt-sensitive and salt-resistant rice lines when subjected to salt stress. salt-resistant lines exhibited higher osnuc1 transcript expression levels than salt-sensitive lines during 0.5% (w/v) nacl salt stress for 6d. two sizes of osnuc1 full-length cdna were found in the rice genome database and northern blot analysi ... | 2013 | 24157209 |
| rice db: an oryza information portal linking annotation, subcellular location, function, expression, regulation, and evolutionary information for rice and arabidopsis. | omics research in oryza sativa (rice) relies on the use of multiple databases to obtain different types of information to define gene function. we present rice db, an oryza information portal that is a functional genomics database, linking gene loci to comprehensive annotations, expression data and the subcellular location of encoded proteins. rice db has been designed to integrate the direct comparison of rice with arabidopsis (arabidopsis thaliana), based on orthology or 'expressology', thus u ... | 2013 | 24147765 |
| how unique is the low oxygen response? an analysis of the anaerobic response during germination and comparison with abiotic stress in rice and arabidopsis. | plants face a variety of environmental stresses and have evolved molecular mechanisms to survive these challenges. one of these stresses is low oxygen conditions, which can occur under flooding conditions. rice (oryza sativa) is somewhat unique for its ability to tolerate and even germinate under low to no oxygen conditions. in this study, we examined global transcriptomic responses over the course of germination and in response to low oxygen and other abiotic stress in rice and arabidopsis (ara ... | 2013 | 24101922 |
| stifdb2: an updated version of plant stress-responsive transcription factor database with additional stress signals, stress-responsive transcription factor binding sites and stress-responsive genes in arabidopsis and rice. | understanding the principles of abiotic and biotic stress responses, tolerance and adaptation remains important in plant physiology research to develop better varieties of crop plants. better understanding of plant stress response mechanisms and application of knowledge derived from integrated experimental and bioinformatics approaches are gaining importance. earlier, we showed that compiling a database of stress-responsive transcription factors and their corresponding target binding sites in th ... | 2013 | 23314754 |
| genome-wide landscape of alternative splicing events in brachypodium distachyon. | recently, brachypodium distachyon has emerged as a model plant for studying monocot grasses and cereal crops. using assembled expressed transcript sequences and subsequent mapping to the corresponding genome, we identified 1219 alternative splicing (as) events spanning across 2021 putatively assembled transcripts generated from 941 genes. approximately, 6.3% of expressed genes are alternatively spliced in b. distachyon. we observed that a majority of the identified as events were related to reta ... | 2013 | 23297300 |
| braving the attitude of altitude: caragana jubata at work in cold desert of himalaya. | the present work was conducted to understand the basis of adaptation in caragana jubata in its niche environment at high altitude cold desert of himalaya. molecular data showed predominance of genes encoding chaperones and those involved in growth and development at low temperature (lt), a major cue operative at high altitude. importantly, these genes expressed in c. jubata in its natural habitat. their homologues in arabidopsis thaliana, oryza sativa, and glycine max did not exhibit similar tre ... | 2013 | 23289064 |
| whole genome identification and analysis of fk506-binding protein family genes in grapevine (vitis vinifera l.). | in plant and animal species fk506-binding protein (fkbp) family genes are important conserved genes and it is defined as the receptors of fk506 and rapamycin, where they work as ppiase and protein folding chaperones. fkbp have been isolated from arabidopsis thaliana, oryza sativa, and zea mays. in grape, twenty-three genes containing the fk506-binding domain (fkbp_c) were first time identified by hmmer and blast research, they were classified into three groups and 17 out of the 23 genes were loc ... | 2013 | 23269629 |
| acquisition, conservation, and loss of dual-targeted proteins in land plants. | the dual-targeting ability of a variety of proteins from physcomitrella patens, rice (oryza sativa), and arabidopsis (arabidopsis thaliana) was tested to determine when dual targeting arose and to what extent it was conserved in land plants. overall, the targeting ability of over 80 different proteins from rice and p. patens, representing 42 dual-targeted proteins in arabidopsis, was tested. we found that dual targeting arose early in land plant evolution, as it was evident in many cases with p. ... | 2013 | 23257241 |
| ontogenetic changes in vitamin c in selected rice varieties. | vitamin c (l-ascorbic acid) is a key antioxidant for both plants and animals. in plants, ascorbate is involved in several key physiological processes including photosynthesis, cell expansion and division, growth, flowering, and senescence. in addition, ascorbate is an enzyme cofactor and a regulator of gene expression. during exposure to abiotic stresses, ascorbate counteracts excessive reactive oxygen species within the cell and protects key molecules, including lipids, proteins, and nucleic ac ... | 2013 | 23466746 |
| genomic distribution of maize facultative heterochromatin marked by trimethylation of h3k27. | trimethylation of histone h3 lys-27 (h3k27me3) plays a critical role in regulating gene expression during plant and animal development. we characterized the genome-wide distribution of h3k27me3 in five developmentally distinct tissues in maize (zea mays) plants of two genetic backgrounds, b73 and mo17. there were more substantial differences in the genome-wide profile of h3k27me3 between different tissues than between the two genotypes. the tissue-specific patterns of h3k27me3 were often associa ... | 2013 | 23463775 |
| low oxygen response mechanisms in green organisms. | low oxygen stress often occurs during the life of green organisms, mostly due to the environmental conditions affecting oxygen availability. both plants and algae respond to low oxygen by resetting their metabolism. the shift from mitochondrial respiration to fermentation is the hallmark of anaerobic metabolism in most organisms. this involves a modified carbohydrate metabolism coupled with glycolysis and fermentation. for a coordinated response to low oxygen, plants exploit various molecular me ... | 2013 | 23446868 |
| widespread long noncoding rnas as endogenous target mimics for micrornas in plants. | target mimicry is a recently identified regulatory mechanism for microrna (mirna) functions in plants in which the decoy rnas bind to mirnas via complementary sequences and therefore block the interaction between mirnas and their authentic targets. both endogenous decoy rnas (mirna target mimics) and engineered artificial rnas can induce target mimicry effects. yet until now, only the induced by phosphate starvation1 rna has been proven to be a functional endogenous microrna target mimic (etm). ... | 2013 | 23429259 |
| a role for more axillary growth1 (max1) in evolutionary diversity in strigolactone signaling upstream of max2. | strigolactones (sls) are carotenoid-derived phytohormones with diverse roles. they are secreted from roots as attractants for arbuscular mycorrhizal fungi and have a wide range of endogenous functions, such as regulation of root and shoot system architecture. to date, six genes associated with sl synthesis and signaling have been molecularly identified using the shoot-branching mutants more axillary growth (max) of arabidopsis (arabidopsis thaliana) and dwarf (d) of rice (oryza sativa). here, we ... | 2013 | 23424248 |
| not2 proteins promote polymerase ii-dependent transcription and interact with multiple microrna biogenesis factors in arabidopsis. | micrornas (mirnas) play key regulatory roles in numerous developmental and physiological processes in animals and plants. the elaborate mechanism of mirna biogenesis involves transcription and multiple processing steps. here, we report the identification of a pair of evolutionarily conserved not2_3_5 domain-containing-proteins, not2a and not2b (previously known as at-negative on tata less2 [not2] and vire2-interacting protein2, respectively), as components involved in arabidopsis thaliana mirna ... | 2013 | 23424246 |
| prevalent role of gene features in determining evolutionary fates of whole-genome duplication duplicated genes in flowering plants. | the evolution of genes and genomes after polyploidization has been the subject of extensive studies in evolutionary biology and plant sciences. while a significant number of duplicated genes are rapidly removed during a process called fractionation, which operates after the whole-genome duplication (wgd), another considerable number of genes are retained preferentially, leading to the phenomenon of biased gene retention. however, the evolutionary mechanisms underlying gene retention after wgd re ... | 2013 | 23396833 |
| the use of vigs technology to study plant-herbivore interactions. | plants employ a large variety of defense strategies to resist herbivores, which require transcriptional reprogramming of cells and profound changes in plant metabolism. due to the large number of genes involved in defense processes, rapid screening strategies are essential for elucidating the contributions of individual genes in the responses of plants to herbivory. however, databases and seed banks of mutant plants which allow rapid retrieval of mutant genotypes are limited to a few model plant ... | 2013 | 23386299 |
| wuschel-related homeobox4 is involved in meristem maintenance and is negatively regulated by the cle gene fcp1 in rice. | the shoot apical meristem is the ultimate source of the cells that constitute the entire aboveground portion of the plant body. in arabidopsis thaliana, meristem maintenance is regulated by the negative feedback loop of wuschel-clavata (wus-clv). although clv-like genes, such as floral organ number1 (fon1) and fon2, have been shown to be involved in maintenance of the reproductive meristems in rice (oryza sativa), current understanding of meristem maintenance remains insufficient. in this articl ... | 2013 | 23371950 |
| locally duplicated ohnologs evolve faster than nonlocally duplicated ohnologs in arabidopsis and rice. | whole-genome duplications (wgds) have recurred in the evolution of angiosperms, resulting in many duplicated chromosomal segments. local gene duplications are also widespread in angiosperms. wgd-derived duplicates, that is, ohnologs, and local duplicates often show contrasting patterns of gene retention and evolution. however, many genes in angiosperms underwent multiple gene duplication events, possibly by different modes, indicating that different modes of gene duplication are not mutually exc ... | 2013 | 23362157 |
| genome-wide analysis of histone modifiers in tomato: gaining an insight into their developmental roles. | histone post-translational modifications (hptms) including acetylation and methylation have been recognized as playing a crucial role in epigenetic regulation of plant growth and development. although solanum lycopersicum is a dicot model plant as well as an important crop, systematic analysis and expression profiling of histone modifier genes (hms) in tomato are sketchy. | 2013 | 23356725 |
| organ evolution in angiosperms driven by correlated divergences of gene sequences and expression patterns. | the evolution of a species involves changes in its genome and its transcriptome. divergence in expression patterns may be more important than divergence in sequences for determining phenotypic changes, particularly among closely related species. we examined the relationships between organ evolution, sequence evolution, and expression evolution in arabidopsis thaliana, rice (oryza sativa), and maize (zea mays). we found correlated divergence of gene sequences and expression patterns, with distinc ... | 2013 | 23341336 |
| atlazy1 is a signaling component required for gravitropism of the arabidopsis thaliana inflorescence. | the present study identified a family of six a. thaliana genes that share five limited regions of sequence similarity with lazy1, a gene in oryza sativa (rice) shown to participate in the early gravity signaling for shoot gravitropism. a t-dna insertion into the arabidopsis gene (at5g14090) most similar to lazy1 increased the inflorescence branch angle to 81° from the wild type value of 42°. rna interference lines and molecular rescue experiments confirmed the linkage between the branch-angle ph ... | 2013 | 23331961 |
| molecular control of flowering in response to day length in rice. | flowering at the most appropriate times of the year requires careful monitoring of environmental conditions and correct integration of such information with an endogenous molecular network. rice (oryza sativa) is a facultative short day plant, and flowers quickly under short day lengths, as opposed to arabidopsis thaliana whose flowering is accelerated by longer days. despite these physiological differences, several genes controlling flowering in response to day length (or photoperiod) are conse ... | 2013 | 23331542 |
| gene body methylation is conserved between plant orthologs and is of evolutionary consequence. | dna methylation is a common feature of eukaryotic genomes and is especially common in noncoding regions of plants. protein coding regions of plants are often methylated also, but the extent, function, and evolutionary consequences of gene body methylation remain unclear. here we investigate gene body methylation using an explicit comparative evolutionary approach. we generated bisulfite sequencing data from two tissues of brachypodium distachyon and compared genic methylation patterns to those o ... | 2013 | 23319627 |
| oself3 is involved in circadian clock regulation for promoting flowering under long-day conditions in rice. | heading date is a critical trait that determines cropping seasons and regional adaptability in rice (oryza sativa). research efforts during the last decade have identified some important photoperiod pathway genes that are conserved between arabidopsis and rice. in this study, we identified a novel gene, oryza sativa elf3 (oself3), which is a putative homolog of the elf3 gene in arabidopsis thaliana. oself3 was required for the control of heading date under long-day conditions. its tos17-tagging ... | 2013 | 22888152 |
| the putative phytocyanin genes in chinese cabbage (brassica rapa l.): genome-wide identification, classification and expression analysis. | phytocyanins (pcs) are a plant-specific family of small copper-containing electron transfer proteins. pcs may bind with a single copper atom to function as electron transporters in various biological systems, such as copper trafficking and plant photosynthesis. evidence indicates that pcs may also be involved in plant developmental processes and stress responses. many pcs possess arabinogalactan protein-like regions and are therefore termed chimeric arabinogalactan proteins (cagps). previously, ... | 2013 | 23212439 |
| identification of the highly accumulated microrna*s in arabidopsis (arabidopsis thaliana) and rice (oryza sativa). | plant micrornas (mirnas) are crucial for the regulation of gene expression, which is involved in almost all the important biological processes. in the cytoplasm, the mirna strand is selectively incorporated into a specific argonaute (ago)-associated gene silencing complex, while the mirna* is degraded rapidly. thus, most mirna*s were thought to be biologically meaningless. interestingly, several recent reports in both plants and animals have shaken this notion. many mirna*s were demonstrated to ... | 2013 | 23201415 |
| transposing from the laboratory to the classroom to generate authentic research experiences for undergraduates. | large lecture classes and standardized laboratory exercises are characteristic of introductory biology courses. previous research has found that these courses do not adequately convey the process of scientific research and the excitement of discovery. here we propose a model that provides beginning biology students with an inquiry-based, active learning laboratory experience. the dynamic genome course replicates a modern research laboratory focused on eukaryotic transposable elements where begin ... | 2013 | 23172853 |
| one divinyl reductase reduces the 8-vinyl groups in various intermediates of chlorophyll biosynthesis in a given higher plant species, but the isozyme differs between species. | divinyl reductase (dvr) converts 8-vinyl groups on various chlorophyll intermediates to ethyl groups, which is indispensable for chlorophyll biosynthesis. to date, five dvr activities have been detected, but adequate evidence of enzymatic assays using purified or recombinant dvr proteins has not been demonstrated, and it is unclear whether one or multiple enzymes catalyze these activities. in this study, we systematically carried out enzymatic assays using four recombinant dvr proteins and five ... | 2013 | 23154534 |
| loose plant architecture1, an indeterminate domain protein involved in shoot gravitropism, regulates plant architecture in rice. | tiller angle and leaf angle are two important components of rice (oryza sativa) plant architecture that play a crucial role in determining grain yield. here, we report the cloning and characterization of the loose plant architecture1 (lpa1) gene in rice, the functional ortholog of the atidd15/shoot gravitropism5 (sgr5) gene in arabidopsis (arabidopsis thaliana). lpa1 regulates tiller angle and leaf angle by controlling the adaxial growth of tiller node and lamina joint. lpa1 was also found to af ... | 2013 | 23124325 |
| nuclear ubiquitin proteasome degradation affects wrky45 function in the rice defense program. | the transcriptional activator wrky45 plays a major role in the salicylic acid/benzothiadiazole-induced defense program in rice. here, we show that the nuclear ubiquitin-proteasome system (ups) plays a role in regulating the function of wrky45. proteasome inhibitors induced accumulation of polyubiquitinated wrky45 and transient up-regulation of wrky45 target genes in rice cells, suggesting that wrky45 is constantly degraded by the ups to suppress defense responses in the absence of defense signal ... | 2013 | 23013464 |
| aldehyde dehydrogenase (aldh) superfamily in plants: gene nomenclature and comparative genomics. | in recent years, there has been a significant increase in the number of completely sequenced plant genomes. the comparison of fully sequenced genomes allows for identification of new gene family members, as well as comprehensive analysis of gene family evolution. the aldehyde dehydrogenase (aldh) gene superfamily comprises a group of enzymes involved in the nad(+)- or nadp(+)-dependent conversion of various aldehydes to their corresponding carboxylic acids. aldh enzymes are involved in processin ... | 2013 | 23007552 |
| plantrna, a database for trnas of photosynthetic eukaryotes. | plantrna database (http://plantrna.ibmp.cnrs.fr/) compiles transfer rna (trna) gene sequences retrieved from fully annotated plant nuclear, plastidial and mitochondrial genomes. the set of annotated trna gene sequences has been manually curated for maximum quality and confidence. the novelty of this database resides in the inclusion of biological information relevant to the function of all the trnas entered in the library. this includes 5'- and 3'-flanking sequences, a and b box sequences, regio ... | 2013 | 23066098 |
| plant growth and cultivation. | there is a variety of methods used for growing plants indoor for laboratory research. in most cases plant research requires germination and growth of plants. often, people have adapted plant cultivation protocols to the conditions and materials at hand in their own laboratory and growth facilities. here i will provide a guide for growing some of the most frequently used plant species for research, i.e., arabidopsis thaliana, barley (hordeum vulgare) and rice (oryza sativa). however, the methods ... | 2013 | 23073874 |